The story just is what it is: to the point and never way too pompously-portrayed, like your average Mario game in terms of how well it stays out of the way. Even then, though, the story is rather complex for a platformer to portray, and this is all shown through a steady, fitting progression through different envinronments, different betrayals, and some climactic moments at the end of the whole affair. Great integration and effective development of ideasthat's what S3&K stands for in Sonic games.
I'm really starting to think that the story aspect really caught on to Takashi Iizuka, who worked on the gameof course, though, he never really understood why it worked, if such was the case. Many middling cutscenes and bad plots later, I don't think he'll ever understand why the story just plain worked, and he tries too hard to set up a plot-infested crapshoot every time. Sonic Adventure was the only really clever thing he ever did with Sonic story-lines, I think, and that was because of the whole Rashomon-like distorted perspective format that was used.